BACKGROUND: Bacterial colonization of the intestine early in life might have implications for allergy development. We studied early host-bacterial interactions in the gut by simultaneous measurements of hydrogen gas (H(2)) and faecal short chain fatty acid pattern (SCFAs), i.e. bacterial products, as well as of nitric oxide (NO), a marker of mucosal immune activation. METHODS: A novel minimally invasive technique was used for repeated measurements of luminal colonic H(2) and NO in 32 healthy newborn infants delivered vaginally or by Caesarean section. Luminal gas was sampled and analysed at five occasions: immediately after birth, day 1, days 3-5, 1 and 5-6 months after birth. RESULTS: Colonic H(2), NO and faecal SCFAs were undetectable at birth. The H(2) and SCFAs appeared within 24 h and continued to increase during the 6 months follow-up. Nitric oxide remained very low until 3-5 days after birth at which time it markedly increased. In some apparently healthy infants NO transiently reached levels similar to those seen in adults with inflammatory bowel disease. CONCLUSION: Intracolonic measurements of H(2) and NO may be useful to monitor the developmental colonization process as well as mucosal responses.